Compound and Protein specific Features

Compound and Protein specific Features

Compound Structure

If a compound identifier is detected in an Excel table and a SMILES string is available in the database the compound structures can be displayed based on the SMILES string.

Compound Search

If a compound identifier is detected in an Excel table the SEEK database can be searched for all data files containing information about the selected compound (click on the compound identifier and select “search in SEEK”). The search result includes not only a list of data files but also data preview from the Excel tables.

The same search can be run by typing the compound identifier into the search input field at the top right corner. leading zeros in the compound identifier can be dropped (e.g. search for NMT-1 instead of NMT-0001) .

Compound Summary Report

The compound summary report can be run by clicking on a compound identifier and choosing the ‘Compound summary report’ option. It contains all available and relevant information extracted from different Excel tables in SEEK.

Protein Links

Proteins in Excel tables given by a UniprotKB_ID are automatically linked to UniprotKB and StringDB.

Compound Structure Search

Compound structures can be searched by clicking on “Structure search” in the blue menu bar. The structure search query can be defined by SMILES or SMARTS strings or by drawing the structure using the JSME editor. The query field will be automatically updated while drawing a structure in the editor.

The search allows three different searches using the tabs for

search for exact structure
including

selection about canonical or non-canonical SMILES

selection about encoded isotopes and stereochemistry

search for substructure
Searched substructures can be highlighted in the chemical structure by clicking on “Highlight substructure match” button(s) below the result structure.

search for similar structure
including

definition of fingerprint size

definition of ingerprint search depth

definition of Tanimoto coefficient cutoff

“Link to this search” offers the possibility to store the query or forward it to other SEEK users.

For selected result entries aditional attributes extracted from other Excel tables in SEEK can be displayed by clicking on “Attributes for selected”. Selected entries can be exported in CSV, Excel, or PDF format or copied/printed directly.